view: A basic 3D image viewer

Description

This function displays one or more 2D or 3D images, with optional click-to-navigate interactivity.

Usage

view(
  ...,
  point = NULL,
  radiological = getOption("radiologicalView", FALSE),
  interactive = base::interactive(),
  crosshairs = TRUE,
  labels = TRUE,
  infoPanel = defaultInfoPanel
)
lyr(
  image,
  scale = "grey",
  min = NULL,
  max = NULL,
  mask = NULL,
  alpha = 1,
  label = NULL,
  dict = NULL
)

Value

lyr returns a list of class "viewLayer", to be used in a view. view is called for its side-effect of showing a view.

Arguments

...: One or more images, or "viewLayer" objects, to display. These will be plotted in the order specified, so that the first image forms the lowest layer.
point: A numeric vector giving the location to initially centre the view on. If crosshairs are in use, they will be placed at this point. For 3D images, this parameter also determines the planes shown in each subview.
radiological: Logical value. If TRUE, images will be displayed in the radiological convention whereby the left of the image is shown on the right; otherwise left is on the left.
interactive: Logical value. If TRUE, the user can navigate around the image by repeatedly clicking on a new centre point; otherwise the view is fixed.
crosshairs: Logical value, indicating whether crosshairs should be shown or not.
labels: Logical value, indicating whether orientation labels should be shown or not. Ignored (defaulting to FALSE) if the image is 2D or orientation information is not available.
infoPanel: A function of three arguments, which must produce a plot for the information panel of the view. defaultInfoPanel is the default, which shows the labels and values of each image at the current point. A NULL value will suppress the panel.
image: The image being shown in this layer.
scale: A character vector of colour values for the scale, or a single string naming a predefined scale: "grey" or "gray" for greyscale, "heat" for a heatmap, "rainbow" for a rainbow scale, or any of the scales defined in the shades package (see ?shades::gradient, if that package is installed). A fixed colour can be used by wrapping a string in a call to I. If a named character vector is given instead, it is taken to be a lookup table assigning specific colours to specific numerical values (named by the value, as for dict), for categorical images such as atlases or parcellations; any value without a matching name will not be shown. Ignored for RGB images.
min, max: The window minimum and maximum for the layer, i.e., the black and white points. These are ignored for RGB images. Otherwise, if NULL, the default, they are taken from the cal_min or cal_max NIfTI header fields. If either is NA, the image has no window stored in its header, or the two values are equal, then the 1st and 99th percentiles of the data are used, with values close to zero rounded to that extreme. If these values are still equal, the untrimmed range of the image data is used.
mask: A optional mask array, which may be of lower dimensionality than the main image. If specified, this is converted to logical mode and pixels that evaluate FALSE will be set to NA for that layer, meaning they will not be plotted. This operation is performed last, and so will not affect auto-windowing.
alpha: A single opacity value, between 0 (fully transparent) and 1 (fully opaque, the default), to apply to the layer's colour scale. Setting this requires the shades package.
label: An optional character string overriding the default label for the layer, which is otherwise obtained by deparsing the image argument.
dict: An optional named vector or list giving a dictionary of labels for particular numerical values in the image, for layers whose values are categorical rather than continuous (e.g., an atlas image with regions of interest indicated by integer codes). Names should be the numeric codes, coerced to strings, and values the corresponding labels. If given, these labels will be shown instead of raw numbers in the default information panel.

Author

Jon Clayden <code@clayden.org>

Examples

Run this code

im <- readNifti(system.file("extdata", "example.nii.gz", package="RNifti"))
view(im, interactive=FALSE)
view(lyr(im, max=800), interactive=FALSE)
view(lyr(im, mask=im<800), interactive=FALSE)